Personal tools

Coexpression cluster:C1963: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:56, 17 September 2013


Full id: C1963_acute_CD14_Neutrophils_Dendritic_CD19_Eosinophils_CD34



Phase1 CAGE Peaks

Hg19::chr5:57787278..57787351,+p1@GAPT
Hg19::chrX:30595876..30595890,-p1@CXorf21
Hg19::chrX:30595907..30595941,-p2@CXorf21
Hg19::chrX:30595959..30595986,-p3@CXorf21
Hg19::chrX:30595997..30596014,-p5@CXorf21


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0016491oxidoreductase activity0.0458024255269045



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell4.45e-86168
angioblastic mesenchymal cell4.45e-86168
hematopoietic oligopotent progenitor cell2.64e-81161
hematopoietic multipotent progenitor cell2.64e-81161
hematopoietic cell5.91e-80177
leukocyte5.58e-76136
myeloid cell1.36e-65108
common myeloid progenitor1.36e-65108
hematopoietic lineage restricted progenitor cell9.95e-63120
nongranular leukocyte6.23e-60115
myeloid leukocyte1.37e-5672
granulocyte monocyte progenitor cell1.57e-5167
myeloid lineage restricted progenitor cell2.88e-4966
macrophage dendritic cell progenitor1.17e-4761
monopoietic cell8.36e-4659
monocyte8.36e-4659
monoblast8.36e-4659
promonocyte8.36e-4659
defensive cell6.99e-4048
phagocyte6.99e-4048
classical monocyte6.00e-3842
CD14-positive, CD16-negative classical monocyte6.00e-3842
lymphocyte of B lineage7.14e-1724
pro-B cell7.14e-1724
mesenchymal cell3.73e-15354
nucleate cell1.53e-1455
connective tissue cell4.69e-14361
lymphocyte5.09e-1453
common lymphoid progenitor5.09e-1453
lymphoid lineage restricted progenitor cell1.84e-1352
stuff accumulating cell2.48e-1387
B cell9.70e-1214
motile cell2.46e-10386
intermediate monocyte2.90e-099
CD14-positive, CD16-positive monocyte2.90e-099
dendritic cell5.76e-0910
granulocyte1.28e-088
conventional dendritic cell2.13e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.48e-5698
blood island5.48e-5698
hemolymphoid system2.47e-50108
bone marrow2.34e-4576
immune system5.54e-4293
bone element5.79e-4082
skeletal element6.04e-3490
skeletal system1.14e-28100
adult organism8.45e-18114
lateral plate mesoderm4.50e-15203
connective tissue5.08e-13371
musculoskeletal system4.82e-09167
blood1.18e-0815
haemolymphatic fluid1.18e-0815
organism substance1.18e-0815
Disease
Ontology termp-valuen
hematologic cancer1.92e-1051
immune system cancer1.92e-1051
myeloid leukemia2.29e-0931
leukemia5.47e-0939


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.12.34794
MA0041.10.64667
MA0042.10.612397
MA0043.12.51533
MA0046.11.10134
MA0048.10.195817
MA0050.16.28581
MA0051.14.20326
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.12.2047
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.12.62998
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.11.8711
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.12.75442
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.12.57792
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.11.63245
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.22.29226
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.11.35623
MA0151.10
MA0152.11.66846
MA0153.11.21379
MA0154.10.514087
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.22.01584
MA0018.20.781393
MA0099.20.699641
MA0079.20.00732454
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL11A#53335422.69556408288567.49488101632307e-060.00021451298395828
BCL3#602427.63768224299073.425174836939e-060.000114215145209155
EBF1#187947.12517347725520.0007230531046774210.00577419660493999
EP300#203345.419153380978560.00209386927943890.0121267461695403
IRF4#3662417.53161014939532.08739444052064e-050.0004610943062046
MEF2A#4205414.99458472771523.876195075647e-050.000728366206379087
NFKB1#479044.390450739355070.004707732692524960.0222093637489662
PAX5#507945.335652424942260.002223389586187790.0127825930304892
POU2F2#545247.284899246194020.0006631223288743860.00542714778663992
RFX5#599349.638328661756080.000221480125815720.00249850538561978
SP1#666744.558705102512720.00407573565781680.0194928679015766
SPI1#668846.563458806818180.0009957429636454020.00714443524183582
YY1#752843.928936599883080.007193866269917620.0298557599588288



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1963&oldid=3069080"